TThhee

RRNNAA

WWoorrldld

E. Westhof http://www-ibmc.u-strasbg.fr/upr9002/westhof/ Stabilization of Fossils of the hydrosphere stromatolites Decrease in the Organic matter Earth Number of From living organisms Formation Meteorite impacts

4.5 4.2 4.0 3.8 3.6 3.4 (x 109 ans) RNA WOLRD Global overview of all life

RNA World The RNA World

• Origin of life / central dogma paradox • DNA needs proteins to replicate • Proteins coded for by DNA • RNA can be code and machinery • Selex, aptamers • RNAs are remnants • Ancient and Essential RNA, Parts

O O

H H N N Bases

O N O N Sugar (ribose) OH OH O O O O O Phosphate O P O O P O - O - 5’ 3’ DNA = modified RNA

O O

-O P O P O Base O Ribonucleoside O- O- H H H H triphosphates RNA OH OH

NADP+ Thioredoxine (-SH)2 Ribonucleoside NADPH diphosphate + Thioredoxine + H -(S-S-) réductase

O O

-O P O P O Base O Deoxyribonucleoside O- O- H H H H triphosphates DNA OH H O O3' O O3' O O3'

P P P

O O5' O O5' O O5' Nucleic acids are negatively charged biopolymers ...

5!’ ADENINE (A) O

O P O O

O O THYMINE (T) (Uracil) OH O P O O O GUANINE (G) O

O P O OH O

O

O OH CYTOSINE (C) O P O O O

O OH O P O RNARNA O 3!’ Conformations of RNA

•Primary structure of RNA similar to DNA

•RNA, like DNA, can be single or double stranded, linear or circular. •Unlike DNA, RNA can exhibit different foldings •Different folds permit the RNAs to carry out specific functions in the cell H

H H N N

C H C N N Charge

énamine imine

H O O delocalization

H C C N N

H H lactame (forme céto) lactime (forme énol) H H + N N

C C Tautomeric N N

forms O O H C H C + N N Cytidine H H H H N N

H H H N pKa = 4,2 N 3 + H+

H O H O N N

S S

O O Uridine H Protonation H H N pKa = 9,2 N 3 + H+

H O H O N N possibilities S S

Adénosine H H H H N N

N N H pKa = 3,5 N N 1 + H H + H

H H N N N N

S S

Guanosine O O H O N N N H pKa = 2,1 H N 7 N 6 pKa = 9,2 N 1 H H H + H H+ H H H N N N N N N N N N H H H

S S S H Guanine O O

N N H N 6 N 1 H H

H H N N N N N N Always H H Never S S

Adénine H H H N N

N N H seen N 6 N 1 H H

N N seen N N

S S

Uracile H O O O

H H H H N 4 N N 3 ou 2 O H O H O H N N N H

S S S

Cytosine H H H H N N N

H H H H N 4 N N 3 ou 2 O H O H O H N N N H

S S S H H N O CH3 N N H H3C Modified bases N N H H H N N N N N H have different S S 1-méthyladénine 7-méthylguanine

O CH3 … N H N H H H N O H H H3C N N N N N H CH 3 N N O O S 2,2,7-triméthylguanine H H N N N N N H H H … 8-oxoadénine 8-oxoguanine

H H N O H H

N N electronic O H O N N H H

H H H H N N N properties N N H H H Fapy-adénine Fapy-guanine H-bond characteristics

N N 1,8 - 2 Å H H N H N d- d+ d- N H O N donneur accepteur O H N C 2,8 - 3 Å H N H 4 O 6 N

C 3 N H N1 G Horizontal N N N O 2 H N 2 Interactions H H O 4 H N6 N

Base pairing. U 3 N H N1 N A N

N In helices O

H H3C O H 4 N 6 Complementary N

T 3 N H N Watson-Crick N 1 A N N O

55 ° 55 ° 10.5 Å Vertical interactions : stacking

H O N H

O N N N O N N H N N H N O N H H N N N N H H H

H N O N H O N N O H N H O O H N N N N

N O O N N H H Stacking forces

• Driving Force : hydrophobic effect. • Not very specific

•Partition in

very polar regions (phosphates) & less polar ones (exocyclic groups of bases) History of the many roles of RNA Central dogma

The flow of genetic information

transcription translation DNA RNA Protein DNA notoriety Short history of RNA

• Late 1800’s - 2nd kind of nucleic acid not in the nucleus (rRNA) • 1920’s - sugar for DNA vs RNA • 1958 - tRNA (Hoagland) • 1960’s - mRNA Relative Amount of RNA in E. coli rRNA 80% tRNA 15% mRNA 5%

RNA

•“Three” different types of RNA

•mRNA - messenger RNA, specifies order of amino acids during protein synthesis

•tRNA - transfer RNA, during translation mRNA information is interpreted by tRNA

•rRNA – ribosomal RNA, combined with proteins aids tRNA in translation Ribosomal RNA (rRNA) Phylogeny of Life using SSU rRNA Discovery of catalytic RNA

• Early 1980’s : • Tom Cech & Sidney Altman • Self-splicing group I introns and • Ribonuclease P P9.2 P9.1 360 P9.1a 380 370 A G G U G G A A A C GUAUG U U A A UC AAG G G U CGC C U CA C C 350 A • • • • • • • • • • • • • • • • • • • • • • • • • • G G UA UA U GA U U A GUUU C U A GCGG A GUG P13'' A U AU GA A U 390 400 340

P9b 330 P9a U A GGG AG U GG A G A A UC C UC UC C C U A G AC A 320 G C P5a G C 5´ U 3´ g C G U a U 130 U A A u A U 200 G C g 120 C G C G U P10 C g P13 190 P13 U A P5 U G C G C G U a U G C G 20 U a 410 A A U U G U u A C A A G u U A G c U A P9.0 A A G C G A P1 A u A C G G c U A C G G u 210 G C A 260 G c 180 G C P5c G C C G 110 A U P4 G C C A C G A A AGGGU A C G U 310 170 A U A C A U G C P7 G U C CG G A 140 U A U P14'' U G A U A A U G U U 160 P6 U A G C C G A A 270 A U C A A A U P5b G C A C A C G U A A G U 220 G U U G G U 100 G C U G U A A A C G P3 C G P6a C G C G A G 150 C G 250 A U A A U U G C A A A 300 U A G G U C G 280 U A U G C G C G P8 230 A U U A A U U A P14 P6b C G P8 C G P14 A U U A G C 240 U U A U 290 A UG U C U A A A P13' 40 P2 90 80 P230 A A A C A C C G U GG A C UA U UG A C G GA A A U U U GG UA U • • • • • • • • • • • • • • • • • • • • • U G C C U GGUA GC U A GU C UU U A A A C C AU P14' C A A A A 50 70 G P2 60 P2.1 Group I self-splicing introns Core structure

9 5 5'

3'

P10

P5 G P9.0

P1 C G P4 5' P7 7

P6 P3

3 P8 2 6

8 CCaatatalylytictic CCoorree ooff GGrroouupp II intronsintrons

Réaction de Transetransestérificationsterification !!

Ribozyme

H O O H

P N

O N OH O H N

OH N

O O G N O O O P

O O O O P 5' O O OH OH 3'

O U O O P OH O O

O U O Exon 5' Second discovery of RNA

• ncRNAs - functional RNA molecules rather than proteins; RNA other than mRNA (ex.XIST) • RNAi - RNA interference • siRNA- active molecules in RNA interference; degrades mRNA (act where they originate) • miRNAs - tiny 21–24-nucleotide RNAs; probably acting as translational regulators of protein-coding mRNAs (regulate elsewhere) Other Roles of RNA

• stRNA - Small temporal RNA; (ex. lin-4 and let-7 in Caenorhabditis elegans : development • snRNA - Small nuclear RNA; includes spliceosomal RNAs • snoRNA - Small nucleolar RNA; most known snoRNAs are involved in rRNA modification • RNA world - RNA as catalyst Central dogma

The flow of genetic information

transcription translation DNA RNA X Protein ncRNA genes

• Genomic dark matter • Ignored by gene prediction methods • Not in EnsEMBL • Computational complexity • ~10% of human gene count? RNA interference

Intricate maturation pathways Implicated in chromatine remodelling Cleavage part of DICER Measuring device for 21 nt ONE Role of RNA in cells

1 Transcription tRNA DNA DNA mRNA Amino RNA acids polymerase RNAr 1 anticodon

protein RNA Polypeptide nucleotides chain 2 2 Translation codon ribosome Proteins mRNA Versatility of RNA functions • Not only messenger RNAs (alternative splicing) • Number & variety of non-coding RNAs : ribosomal RNAs, snRNAs, snoRNAs,and numerous regulator RNAs.. • Cofactor RNAs : telomerase, • …… to be discovered Properties of RNA molecules

Assemble in double-starnded helices like DNA

Carry GENETIC INFORMATION like DNA

Fold in complex tertiary architectures like proteins

Perform CHEMICAL CATALYSIS like proteins Catalytic RNAs • Ribonuclease P • Self-splicing introns • Hepatitis delta virus • The ribosome and peptide bond formation • The spliceosome (not fully proven yet) • and ... Great diversity of RNA functions and architectures

Genome

Transfer RNA Ribozyme 2D2D 3D3D

DDifferentifferent levelslevels ooff organizationorganization possiblypossibly hhieraierarcrchhicicaallylly ststruruccttuuredred.. TThehe bbacterialacterial ribriboososommee ::

270270 000000 aattoommss ((CC,,NN,, OO,, PP)) 5555 proteinsproteins 33 RRNNAA (4(4660000 nnuuccleleoottidideess)) Ribosome active site

30S 50S

Nissen et al. (2000) Science, 289

H. F. Noller, T. A. Steitz, P. B. Moore, A.Yonath, V. Ramakrishnan Luc Jaeger © Only RNA in the reaction site Comparisons of 3D structures

Comparisons of sequences

(((( ((( ))) )))-) GCUG UUAGG GGA GUUUUA UCC AGCGU CAG-C GCCG UUAGG GGA GUUUCA UCC AGCGA UGG-C GUUG UAGG GGA GUCUCA UCC AGCA CAA-C GCUG GAGG GAA GC AA UUC AGCA CAG-C ACUU CAGU GGA GC AA UCC AGCA GAGAU ACUU CAGU GGA GC AA UCC AGCA GAGAU GAUG GAGG UUG G AAA CAA UGCA CAU-C GGGC CAGG GGU G AAA ACC AGCA GCC-A GGCC UAGG UCG G AAA CGG AGCA GGU-C GGCC CAGG UCG G AAA CGG AGCA GGU-C GGCC CAGG UCG G AAA CGG AGCA GGU-C GGCC CAGG UCG G AAA CGG AGCA GGU-C GGCC CAGG UCG G AAA CGG AGCA GGU-C Biological sequence analysis

Protein easy RNA hard Watson-Crick base paired helices 2D2D

Internal loops (symmetric, Asymmetric, bulge)

Hairpin loops

Single-strands junctions RNA alignments

• RNA sequences are aligned/compared differently because sequence variation in RNA maintain base-pairing patterns • Thus an alignment will exhibit covariation at interacting basepairs

• RNA specifying genes will have conserved regions reflecting common ancestry Main building block : the RNA double helix held together by Watson-Crick pairs